Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2058
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25627
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Found at i:6084 original size:28 final size:28
Alignment explanation
Indices: 6053--6110 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
6043 TCATCTTATA
6053 TATATATATAACGAATAGGTACTTGTAT
1 TATATATATAACGAATAGGTACTTGTAT
*
6081 TATATATATAACGACTAGGTACTTGTAT
1 TATATATATAACGAATAGGTACTTGTAT
6109 TA
1 TA
6111 CTCACGTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (28 bp):
TATATATATAACGAATAGGTACTTGTAT
Found at i:6307 original size:46 final size:47
Alignment explanation
Indices: 6220--6392 Score: 178
Period size: 46 Copynumber: 3.7 Consensus size: 47
6210 GGTAGGATGG
* *
6220 CGATGCCATGTCTCAGACATCGTCTTACACTGGC-TCATCTCGTA-GC
1 CGATGCCATGTCCCAGACATCGTCTTACACTAGCTTCATCTCG-AGGC
*
6266 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTTACATCTCGAGGT
1 CGATGCCATGTCCCAGACATCGTCTTACACTAGCTT-CATCTCGAGGC
* * * *
6312 TGATG-CATGTCCCAGACAT-GTCTTACACCAGCTCTCATCTCAATGC
1 CGATGCCATGTCCCAGACATCGTCTTACACTAGCT-TCATCTCGAGGC
** * *
6358 TAATGCCATGTCCCAGACGTGGTCTTACACTAGCT
1 CGATGCCATGTCCCAGACATCGTCTTACACTAGCT
6393 CACAATAGCC
Statistics
Matches: 110, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
44 12 0.11
45 15 0.14
46 56 0.51
47 14 0.13
48 13 0.12
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATCGTCTTACACTAGCTTCATCTCGAGGC
Found at i:8790 original size:40 final size:40
Alignment explanation
Indices: 8715--8800 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
8705 ACTCTGTATC
* * *
8715 TCGCACACTAAGTGTCGTACATAGCCGAAGCTATCTTAAA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCAAA
* * * *
8755 TCGCACACTAAGTGCCATATATTGCGGAAGTTATCTCAAA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCAAA
*
8795 TAGCAC
1 TCGCAC
8801 TGTAGTCTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCAAA
Found at i:11389 original size:39 final size:40
Alignment explanation
Indices: 11232--11456 Score: 251
Period size: 40 Copynumber: 5.7 Consensus size: 40
11222 GCTACTCGTT
* * *
11232 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
11272 CAAATGTCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
11312 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
11352 CCAATGCATTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
11391 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
11432 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
11457 CATCATTCGA
Statistics
Matches: 160, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 114 0.71
41 13 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:11416 original size:119 final size:120
Alignment explanation
Indices: 11234--11456 Score: 274
Period size: 119 Copynumber: 1.9 Consensus size: 120
11224 TACTCGTTCA
* * * *
11234 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTTGCACAAATGTCTTCGGGACTTAACCCGGAT
1 AATGCATTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
11299 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
11354 AATGCATTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCATTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
11416 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
11457 CATCATTCGA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
118 4 0.05
119 64 0.74
120 19 0.22
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (120 bp):
AATGCATTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:18110 original size:39 final size:39
Alignment explanation
Indices: 18031--18246 Score: 247
Period size: 39 Copynumber: 5.5 Consensus size: 39
18021 GCTACTCGTT
* *
18031 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAACCCGGATT-TAGTAACTCGCA
*
18071 CAAATGCCTTCGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
18110 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
18150 CCAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
18189 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAACCCGGATTTAGTAAC-TCGCA
18230 CAAA-GCCTTCGGACTTA
1 CAAATGCCTTCGGACTTA
18247 GCCTGGACAT
Statistics
Matches: 154, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
39 73 0.47
40 73 0.47
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:18134 original size:79 final size:79
Alignment explanation
Indices: 18031--18246 Score: 267
Period size: 79 Copynumber: 2.7 Consensus size: 79
18021 GCTACTCGTT
*
18031 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGACTTAACCCAGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGACTTAACCCAGA
*
18096 TTTAGTAACTCGCA
66 ATTAGTAACTCGCA
* * * * *
18110 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGACTTAACCCAG
*
18174 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * * *
18189 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGACTTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGACTTA
18247 GCCTGGACAT
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
78 4 0.03
79 104 0.89
80 9 0.08
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGACTTAACCCAGA
ATTAGTAACTCGCA
Found at i:20677 original size:40 final size:40
Alignment explanation
Indices: 20452--20677 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
20442 GCTACTCGTT
*
20452 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
20492 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
20532 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
20572 CAAATGCCTTC-GGATCTTAGTCCAGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
20612 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AACTCGCA
20653 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20678 CATCATTCAA
Statistics
Matches: 167, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
39 3 0.02
40 150 0.90
41 14 0.08
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:23473 original size:146 final size:146
Alignment explanation
Indices: 23209--23502 Score: 579
Period size: 146 Copynumber: 2.0 Consensus size: 146
23199 TGACATATGG
23209 CATAAAAATCGTATTACCAAGACTTACGACCCAACATTAGAACCAAATTCAACCGAACATTATGC
1 CATAAAAATCGTATTACCAAGACTTACGACCCAACATTAGAACCAAATTCAACCGAACATTATGC
23274 CATTTTCGCATGGCTAAAAGTTTACATACCAAATTTCAACAAAACATATTAGCCTATACATGCCG
66 CATTTTCGCATGGCTAAAAGTTTACATACCAAATTTCAACAAAACATATTAGCCTATACATGCCG
23339 AAATGTTCTCTTAGAC
131 AAATGTTCTCTTAGAC
23355 CATAAAAATCGTATTACCAAGACTTACGACCCAACATTAGAACCAAATTCAACCGAACATTATGC
1 CATAAAAATCGTATTACCAAGACTTACGACCCAACATTAGAACCAAATTCAACCGAACATTATGC
*
23420 CATTTTCGCATGGCTAAAAGTTTACATACCAAATTTCAACAAAACATTTTAGCCTATACATGCCG
66 CATTTTCGCATGGCTAAAAGTTTACATACCAAATTTCAACAAAACATATTAGCCTATACATGCCG
23485 AAATGTTCTCTTAGAC
131 AAATGTTCTCTTAGAC
23501 CA
1 CA
23503 ACTAAGAAGA
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 147 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (146 bp):
CATAAAAATCGTATTACCAAGACTTACGACCCAACATTAGAACCAAATTCAACCGAACATTATGC
CATTTTCGCATGGCTAAAAGTTTACATACCAAATTTCAACAAAACATATTAGCCTATACATGCCG
AAATGTTCTCTTAGAC
Found at i:24132 original size:28 final size:28
Alignment explanation
Indices: 24069--24250 Score: 294
Period size: 28 Copynumber: 6.5 Consensus size: 28
24059 ATATTAAGTC
* *
24069 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
24096 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
24124 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
24152 CGCACACCTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
*
24180 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
24208 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
24236 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
24251 GTACAATTTA
Statistics
Matches: 147, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
27 22 0.15
28 125 0.85
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Done.